Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献

{"title":"Multomics decipher the mechanisms of bisphenol S-induced oxidative stress and inflammation in Pseudobagrus ussuriensis","authors":"Lu Wang ,&nbsp;Changchang Pu ,&nbsp;Yimin Li ,&nbsp;Jiaxiang Zhu ,&nbsp;Mohammad Mehdi Ommati ,&nbsp;Bingke Wang ,&nbsp;Chunnuan Zhang","doi":"10.1016/j.cbd.2025.101725","DOIUrl":"10.1016/j.cbd.2025.101725","url":null,"abstract":"<div><div>Bisphenol S (BPS), a widespread environmental endocrine-disrupting chemical, has raised growing concerns regarding its ecotoxicological effects. In this study, we systematically investigated the integrated toxicity of BPS exposure using <em>Pseudobagrus ussuriensis</em> as a model aquatic species. Three hundred sixty fish (mean initial weight: 30.42 ± 0.62 g) were randomly allocated into four groups and exposed to 0 (control), 1, 10, or 100 μg/L BPS for 14 days. Histopathological examination revealed significant tissue damage, including gill filament edema, intestinal epithelial desquamation, and hepatic vacuolization. Oxidative stress assessment showed a concentration-dependent elevation in malondialdehyde (MDA) levels (<em>p</em> &lt; 0.05). 16S rRNA sequencing analysis demonstrated that 10 μg/L BPS exposure markedly altered gut microbial composition, with significant enrichment of <em>Achromobacter</em> and <em>Acinetobacter</em>. Liver transcriptome profiling identified substantial differential expression of immune-related genes (<em>hmgb1</em>, <em>nfκb</em>, and <em>nfκbiα</em>) in the 100 μg/L exposure group. Importantly, Pearson correlation analysis established a significant association between gut microbiota perturbation and hepatic immune-inflammatory responses (<em>p</em> &lt; 0.05). To our knowledge, this study provides the first evidence that environmentally relevant concentrations (10 μg/L) of BPS can induce significant physiological impairments in <em>P. ussuriensis</em>, offering novel insights into the ecological risks of BPS contamination.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101725"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145738493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential expression miRNAs in the gonad of sea cucumber Holothuria leucospilota","authors":"Jing Zhang ,&nbsp;Xiao-qin Fu ,&nbsp;Run-xin Lin ,&nbsp;Yang Zhang ,&nbsp;Pei-ming Zheng ,&nbsp;Huo Li","doi":"10.1016/j.cbd.2025.101711","DOIUrl":"10.1016/j.cbd.2025.101711","url":null,"abstract":"<div><div>MicroRNAs are defined as a class of short noncoding RNAs, which play important function in cell differentiation, developmental process and gender determination. The sea cucumber <em>Holothuria leucospilota</em> is a member of the Echinodermata, known for its excellent nutritional and economic value. Breeding efficiency of sea cucumbers is low due to the difficulty in distinguishing between male and female individuals. Discovering molecular markers that distinguish between genders will provide a robust strategy for elucidating the genetic mechanisms governing gender determination and differentiation. In this investigation, high-throughput sequencing was utilized to compare miRNA expression patterns in the gonadal tissues of male and female specimens of <em>H. leucospilota</em>. A total of 584 known miRNAs and 404 novel miRNAs were identified, of which 97 miRNAs were identified as significantly differentially expressed miRNAs (DEMs) between male and female sea cucumbers. These findings enabled the construction of a miRNA-mRNA regulatory network. Pathway analysis of target genes highlighted the potential roles of neuroactive ligand-receptor interactions, calcium signaling, Salmonella infection, endocytosis, and MAPK signaling in governing gender differentiation processes. The expression results of high-throughput sequencing were validated in sc-miR121, sc-miR41, sc-miR67, sc-miR90, sc-miR104 and sc-miR189 by quantitative real-time quantity polymerase chain reaction (RT-qPCR). In summary, our results will provide a foundation for future studies of miRNA regulation in gender differentiation of sea cucumber <em>H. leucospilota</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101711"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145738489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The SoxE gene family in Siniperca scherzeri: Systematic characterization, spatiotemporal expression, and sexual dimorphism in early gonads","authors":"Binhua Deng,&nbsp;Dingxian Chen,&nbsp;Shengyue Lin,&nbsp;Jiayu Li,&nbsp;Haiying Yang,&nbsp;Guojun Cai,&nbsp;Ziyan Deng,&nbsp;Zihang Xie,&nbsp;Lilin Zhan,&nbsp;Chong Han,&nbsp;Qiang Li","doi":"10.1016/j.cbd.2026.101770","DOIUrl":"10.1016/j.cbd.2026.101770","url":null,"abstract":"<div><div>This study systematically identified all six members of the <em>soxE</em> gene family (<em>sox8a</em>, <em>sox8b</em>, <em>sox9a</em>, <em>sox9b</em>, <em>sox10a</em>, <em>sox10b</em>) in <em>Siniperca scherzeri</em> for the first time. Their conserved HMG-box domains were confirmed through bioinformatics analysis. The expression patterns of these genes were analyzed across different tissues of adult fish and during various stages of gonad development. Additionally, the effects of 17α-methyltestosterone (MT) immersion treatment during the critical period of sex differentiation on <em>soxE</em> genes expression and gonad development were investigated. The results revealed that the expression levels of all <em>soxE</em> genes were significantly higher in male individuals, particularly in the testes, compared to females, indicating pronounced sexual dimorphism. Specifically, MT treatment significantly upregulated the expression of <em>sox9a</em> and <em>sox9b</em>, accompanied by an increase in the expression of the male-related gene <em>dmrt1</em> and a decrease in the expression of the female-related gene <em>cyp19a1a</em>, thereby inducing sex reversal in genetic females. These findings suggest that the <em>soxE</em> gene family, particularly the two isoforms of <em>sox9</em>, may play crucial roles in male sex determination, gonad development, and the regulatory network of sex differentiation in <em>Siniperca scherzeri</em>, providing an important molecular foundation for understanding its sex determination mechanisms.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101770"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146159574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Serine proteases and serine protease inhibitors identified from the venom gland transcriptome of Rhitymna verruca","authors":"Zhi Li,&nbsp;Mengmeng Zhang,&nbsp;Wenhao Yin,&nbsp;Yulin Zheng,&nbsp;Heng Liu,&nbsp;Yu Zhao,&nbsp;Zizhong Yang","doi":"10.1016/j.cbd.2025.101719","DOIUrl":"10.1016/j.cbd.2025.101719","url":null,"abstract":"<div><div><em>Rhitymna verruca</em> is a large nocturnal wandering spider and an important natural predator of agricultural and forestry pests, with its venom playing a key role in prey capture. However, systematic studies on the composition of its venom remain scarce. In this study, we performed an integrated analysis of the venom gland and venom samples using high-throughput transcriptome sequencing combined with quantitative proteomics. The transcriptome yielded 43,244 representative unigene sequences, among which 102 toxin-like sequences were identified through functional annotation, encompassing 13 peptide toxin superfamilies and 7 protein toxin families. Proteomic analysis identified 35 venom components, including 14 peptide toxins and 21 functional proteins. The most abundantly expressed toxin families, Superfamily IX and VII, were highly expressed at both transcriptomic and proteomic levels, suggesting central roles in prey paralysis and neuroregulation. Most peptide toxins possessed ICK or Kunitz domains, indicating high structural stability and potential target specificity. In addition, the venom was rich in auxiliary components such as CAP protein superfamily, hyaluronidases, and metalloproteases, which may contribute to toxin synergy, diffusion, and tissue disruption. This study provides the first comprehensive characterization of the venom composition of <em>R. verruca</em>, offering fundamental insights into its functional mechanisms, evolutionary patterns, and potential applications in the development of novel bioactive agents.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101719"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145822342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Incorporating GWAS-derived prior information enhances genomic prediction for body size traits in the mud crab (Scylla paramamosain)","authors":"Weiren Zhang ,&nbsp;Jun Luo ,&nbsp;Yijia Shih ,&nbsp;Yaodong Zhang ,&nbsp;Siyi Zhou ,&nbsp;Qionghui Qin ,&nbsp;Kewei Huang ,&nbsp;Qi Wang ,&nbsp;Xiaopeng Wang ,&nbsp;Haihui Ye","doi":"10.1016/j.cbd.2025.101704","DOIUrl":"10.1016/j.cbd.2025.101704","url":null,"abstract":"<div><div><em>Scylla paramamosain</em> is an economically important marine crab species in Asia, yet the genetic architecture of its growth traits remains poorly characterized. This study employed an integrated approach combining genome-wide association studies (GWAS) and genomic prediction to dissect the genetic basis of four body size traits (carapace width, carapace length, posterior width of carapace, and body height) in 346 individuals genotyped at 3.9 million high-confidence SNPs. GWAS identified five pleiotropic loci and six candidate genes (including <em>Exportin-5</em> and <em>FANCI</em>) shared among traits, with KEGG enrichment analysis underscoring the importance of metabolic pathways, particularly the citrate cycle. We further evaluated the genomic prediction performance of the GFBLUP model using two types of prior biological knowledge: functionally annotated SNPs derived from the top-enriched KEGG pathways, and trait-associated SNPs selected under varying GWAS significance thresholds. GFBLUP using trait-associated SNPs significantly outperformed standard GBLUP, with prediction accuracy gains of 0.528–0.888. Prediction accuracy increased with SNP panel size, exceeding 0.819 for all traits with the top 1000 SNPs and stabilizing beyond 5000 SNPs (0.837–0.865). An FDR threshold of 0.05 offered an optimal balance, achieving high accuracy (0.840–0.862) with a practical number of SNPs (7980–9302). In contrast, functionally informed GFBLUP provided only modest improvements (0.020–0.197), likely due to the inclusion of non-causal variants. These results demonstrate that low-density SNP panels informed by GWAS prior knowledge substantially enhance genomic prediction for body size traits in <em>S. paramamosain</em>, providing a practical breeding strategy and valuable insights into the genetic mechanisms of growth in non-model crustaceans.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101704"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145727731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive transcriptomic analysis reveals detoxification gene expansion and adaptive genetic variation in the emerging pest Acanthotomicus suncei","authors":"Lulu Dai,&nbsp;Jiao Li,&nbsp;Weiyi Pan,&nbsp;Fangyuan Shen,&nbsp;Dejun Hao","doi":"10.1016/j.cbd.2026.101749","DOIUrl":"10.1016/j.cbd.2026.101749","url":null,"abstract":"<div><div>The bark beetle <em>Acanthotomicus suncei</em> is an emerging destructive pest of the introduced American sweetgum (<em>Liquidambar styraciflua</em>) in China. The molecular mechanisms underlying its successful adaptation to this exotic host, particularly its ability to overcome plant chemical defenses, remain largely unknown. We conducted a comprehensive transcriptomic analysis of <em>A. suncei</em>. Our assembly yielded 30,557 unigenes (N50 = 2175 bp). We identified a significant expansion of genes within three major detoxification enzyme families: 122 cytochrome P450 monooxygenases (P450s), 75 carboxylesterases (COEs), and 47 glutathione S-transferases (GSTs). This repertoire is notably larger than that of many compared curculionid beetles. Phylogenetic analyses revealed complex evolutionary relationships, with <em>A. suncei</em> clustering closely with <em>Dendroctonus</em> species in some P450 and GST clades, while showing considerable divergence in others. Furthermore, we uncovered abundant genetic variation, with single nucleotide polymorphisms (SNPs) being highly prevalent within the coding sequences of these detoxification genes, especially P450s. Simple sequence repeat (SSR) analysis indicated a predominance of A/T-rich motifs. The remarkable expansion and substantial genetic variation observed in the detoxification gene families of <em>A. suncei</em> provide a compelling molecular basis for its potent detoxification capacity. These findings suggest that an enriched and highly adaptable detoxification system likely facilitates this beetle's successful colonization of the exotic host L. <em>styraciflua</em>. This study offers crucial insights into the molecular mechanisms of host adaptation in an emerging forest pest and identifies potential genetic targets for future management strategies.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101749"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145977222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic analysis of the mantle of Manila clam Ruditapes philippinarum reveals the molecular basis of biomineralization during shell regeneration","authors":"Yunze Zhang ,&nbsp;Yaning Li ,&nbsp;Hongtao Nie","doi":"10.1016/j.cbd.2026.101757","DOIUrl":"10.1016/j.cbd.2026.101757","url":null,"abstract":"<div><div>Biomineralization in mollusks, particularly shell formation and repair, is a dynamic process mediated by shell matrix proteins and tightly regulated gene expression. In this study, we investigated the temporal transcriptomic profiles of mantle tissue in the Manila clam (<em>Ruditapes philippinarum</em>) during shell repair. Experimental shells were artificially damaged in a V-shaped pattern, and regeneration was monitored at short-term (48 h), long-term (18 d), and control group (cn) using RNA-seq and qPCR analysis. Scanning electron microscopy (SEM) revealed a sequential reconstruction of the periostracum, prismatic, and nacreous layer, reflecting the temporal organization of mineral deposition. Transcriptomic analysis identified stage-specific differentially expressed genes (350 in m48h vs cn, 163 in m18d vs cn, and 119 in m48h vs m18d) enriched in pathways associated with tyrosine metabolism, chitin biosynthesis, and extracellular matrix (ECM) regulation. Early-stage repair was characterized by rapid upregulation of <em>Pif</em>, <em>Tem</em>, and chitin-binding domain genes, facilitating the formation of organic scaffolds for CaCO₃ crystallization. In later stages, <em>DPT</em> downregulation and reduced ECM-related gene expression, alongside sustained <em>Pif</em> activity, suggest a regulatory mechanism to balance ECM assembly and mineralization. Additionally, upregulation of <em>Pax7</em> and tyrosine metabolism genes indicates an integration of biomineralization processes with shell structural repair. These findings provide new insights into the molecular networks orchestrating bivalve shell regeneration and identify potential genetic targets for strengthening shell robustness in aquaculture and enhancing resilience to environmental stressors such as ocean acidification.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101757"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146077409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Physiological response and transcriptomics study of three Litopenaeus vannamei populations to alkaline stress and recovery","authors":"Rui Xu ,&nbsp;Yongkang Hou ,&nbsp;Yexin Lei ,&nbsp;Jianyong Liu ,&nbsp;Dekhkonova Dilorakhon Rasuljon Kizi","doi":"10.1016/j.cbd.2026.101766","DOIUrl":"10.1016/j.cbd.2026.101766","url":null,"abstract":"<div><div>The development of alkali-tolerant shrimp strains is crucial for sustainable aquaculture in saline-alkaline waters. However, the population-specific genetic basis of alkali tolerance remains poorly understood. This study investigated the immuno-physiological and transcriptomic responses of three <em>Litopenaeus vannamei</em> populations (DF, XH and SIS) to alkaline stress (AG, 15 mmol/L alkalinity for 72 h), and recovery (AR, post-stress return to 1.2 mmol/L for 72 h). Alkaline stress induced significant gill and hepatopancreas damage, characterized by structural distortion and vacuolization. Physiologically, stress suppressed antioxidant capacity (SOD, CAT, GSH-Px) and elevated lipid peroxidation (MDA), while simultaneously activating immune defenses (increased ACP and ALP activities) and disturbing osmoregulation (altered NKA and CA activities). During recovery, tissue integrity and antioxidant capacity improved, and immune/osmoregulatory indicators partially recovered, though not fully to control levels. Transcriptomic analysis revealed population-specific response strategies: The XH (4932 and 4435 DEGs during stress and recovery, respectively) maintains homeostasis via synergistic activation of oxidative phosphorylation and glutathione metabolism across both stages to mitigate oxidative stress; The DF (13,047 and 2579 DEGs) activates innate immunity through pathways like C-type lectin receptor signaling under stress and relied on arachidonic acid metabolism-involved metabolic adaptation during recovery; The SIS population (11,842 and 3351 DEGs) potentially undergoes insulin-PI3K-Akt-mTOR-driven immunometabolic reprogramming under alkaline stress, and may mediate epithelial barrier repair via, for example, the Rap1 signaling pathway and other related pathways during the recovery phase. WGCNA identified 23 hub genes (e.g., <em>APOD</em>, <em>ARSB</em>, <em>RPS15/19/5</em>, <em>SORD</em>) that coordinate stress adaptation by immune responses, oxidative damage alleviation, and regulating energy metabolism. This study reveals dynamic changes in gene expression profiles and regulatory networks of different <em>L. vannamei</em> populations during acute alkaline stress and short-term recovery, providing key theoretical basis for elucidating their alkali tolerance molecular mechanisms.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101766"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146173235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Knockout of zebrafish Clec3bb does cause vertebra density reduction","authors":"Feilong Shi ,&nbsp;Xudong Wang ,&nbsp;Yulong Chen ,&nbsp;Zhengyu Xiao ,&nbsp;Xuemei Xiong ,&nbsp;Jianbo Wang ,&nbsp;Zexia Gao ,&nbsp;Chunhong Nie","doi":"10.1016/j.cbd.2025.101726","DOIUrl":"10.1016/j.cbd.2025.101726","url":null,"abstract":"<div><div>C-type lectin domain family 3 member B (Clec3b) is widely involved in various biological processes, including bone mineralization, cell proliferation, and pathogenesis of diseases. While <em>clec3b</em> association with skeletal development has been well characterized in mammals, its role in fish skeletal development remains unclear. Due to genome duplication in teleosts, zebrafish possess two paralogous genes of <em>clec3b</em>, namely <em>clec3ba</em> and <em>clec3bb</em>, whose functional divergence remains unclear. The amino acid sequence similarity between zebrafish <em>clec3ba</em> and <em>clec3bb</em> was 55.61 %. Tissue-specific expression analysis revealed distinct expression patterns of <em>clec3ba</em> and <em>clec3bb</em> across multiple tissues (brain, gonads, fin, skin, vertebra, eyes, ribs, muscle, kidney, liver, gills) and embryonic stages. Mutants of <em>clec3ba</em> and <em>clec3bb</em> were generated using CRISPR/Cas9 system. Micro-CT analysis revealed that vertebral bone density was significantly reduced in <em>clec3bb</em>⁻/⁻ mutants compared to wild type, whereas no significant change was observed in <em>clec3ba</em>⁻/⁻ mutants. Comparative transcriptome was used to analyze gene expression differences of vertebrae in <em>clec3bb</em>^+/+ and <em>clec3bb</em>⁻/⁻ zebrafish and identified 3316 differentially expressed genes were in vertebral tissues of <em>clec3bb</em> mutants, which were mainly enriched in the MAPK, TGF-β, Calcium and Wnt signaling pathways. RT-qPCR validated results showed that 10 skeletal-related genes (<em>col1a1a</em>, <em>entpd5a</em>, <em>fgf23</em>, <em>bmp6</em>, <em>aspn</em>, <em>bglapl</em>, <em>tnmd</em>, <em>scxa</em>, <em>sp7</em>, <em>tnc</em>) had a lower expression in vertebrae of <em>clec3bb</em>^−/− mutant. The above results highlight the critical role of <em>clec3bb</em> in zebrafish bone mineralization, providing insights into the functional specialization of <em>clec3b</em> paralogs and a theoretical basis for understanding skeletal development mechanisms in teleosts.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101726"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145791276","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative transcriptome analysis provides novel insights into the evolution of enhanced cold tolerance in the northward invasion of the eel goby, Taenioides sp.","authors":"Jing Liu,&nbsp;An Xu,&nbsp;Tianwei Liu,&nbsp;Kun Huang,&nbsp;Weihu Zhu,&nbsp;Jing Yu,&nbsp;Yijing Yang,&nbsp;Fenghui Li,&nbsp;Denghui Zhu,&nbsp;Li Gong,&nbsp;Liqin Liu,&nbsp;Zhenming Lü","doi":"10.1016/j.cbd.2025.101709","DOIUrl":"10.1016/j.cbd.2025.101709","url":null,"abstract":"<div><div>Invasive species serve as an ideal model for investigating adaptation, since they are typically introduced to unfamiliar environments where adaptation is essential for survival. <em>Taenioides</em> sp. is a typical invasive eel goby that originally inhabited the tropical and subtropical coasts of Southeast China but has recently expanded into the temperate regions of North China due to the implementation of ESNT Project. However, the molecular basis underlying how the invasive population adapted to the climate of northern China during the invasion remains largely unknown. Here, we compared the cold tolerance and transcriptomic changes to cold stress in source (Yangtze River estuary) and northernmost invasive (Zhaoyang Lake) populations to elucidate the possible molecular mechanisms underlying this climate adaptation. Our results revealed significantly enhanced cold tolerance in the invasive compared to the source population (CT_min: 7.11 °C vs 10.66 °C). Transcriptome analysis revealed 56 differentially expressed genes (DEGs) with similar expression patterns across all tissues and populations, suggesting their core roles in the cold response of <em>Taenioides</em> sp. Meanwhile, multiple DEGs exhibit population-specific expression profiles, indicating their involvement in divergent cold tolerance. Further WGCNA analyses revealed a subset of cold-response hub genes associated with muscle structure and thermogenesis (e.g., <em>MYO18B</em>) exhibiting a distinct expression profile in the invasive population under cold stress, highlighting their roles in the evolution of enhanced cold tolerance. Our findings provided novel insights into the molecular basis of thermal adaptation underpinning the northward invasion of <em>Taenioides</em> sp. in a hydraulic-project-facilitating context, thus had important implications for predicting their invasive potential and developing management strategies for their effective control. Further analyses regarding how genetic and epigenetic forces have driven population-distinct gene expression regulation and, hence, divergent thermal adaptation will be necessary in the future.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"58 ","pages":"Article 101709"},"PeriodicalIF":2.2,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145791247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}